1dak
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:1dak.gif|left|200px]] | + | [[Image:1dak.gif|left|200px]] |
| - | + | ||
| - | '''DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE''' | + | {{Structure |
| + | |PDB= 1dak |SIZE=350|CAPTION= <scene name='initialview01'>1dak</scene>, resolution 1.6Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=DPU:MIXED+CARBAMIC+PHOSPHORIC+ACID+ANHYDRIDE+OF+7,8-DIAMINONONANIC+ACID'>DPU</scene> and <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1DAK is a [ | + | 1DAK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DAK OCA]. |
==Reference== | ==Reference== | ||
| - | Snapshot of a phosphorylated substrate intermediate by kinetic crystallography., Kack H, Gibson KJ, Lindqvist Y, Schneider G, Proc Natl Acad Sci U S A. 1998 May 12;95(10):5495-500. PMID:[http:// | + | Snapshot of a phosphorylated substrate intermediate by kinetic crystallography., Kack H, Gibson KJ, Lindqvist Y, Schneider G, Proc Natl Acad Sci U S A. 1998 May 12;95(10):5495-500. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9576910 9576910] |
[[Category: Dethiobiotin synthase]] | [[Category: Dethiobiotin synthase]] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
| Line 28: | Line 37: | ||
[[Category: phoshporyl transfer]] | [[Category: phoshporyl transfer]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:35:25 2008'' |
Revision as of 08:35, 20 March 2008
| |||||||
| , resolution 1.6Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , and | ||||||
| Activity: | Dethiobiotin synthase, with EC number 6.3.3.3 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE
Overview
The ATP-dependent enzyme dethiobiotin synthetase from Escherichia coli catalyses the formation of dethiobiotin from CO2 and 7, 8-diaminopelargonic acid. The reaction is initiated by the formation of a carbamate and proceeds through a phosphorylated intermediate, a mixed carbamic phosphoric anhydride. Here, we report the crystal structures at 1.9- and 1.6-A resolution, respectively, of the enzyme-MgATP-diaminopelargonic acid and enzyme-MgADP-carbamic-phosphoric acid anhydride complexes, observed by using kinetic crystallography. Reaction initiation by addition of either NaHCO3 or diaminopelargonic acid to crystals already containing cosubstrates resulted in the accumulation of the phosphorylated intermediate at the active site. The phosphoryl transfer step shows inversion of the configuration at the phosphorus atom, consistent with an in-line attack by the carbamate oxygen onto the phosphorus atom of ATP. A key feature in the structure of the complex of the enzyme with the reaction intermediate is two magnesium ions, bridging the phosphates at the cleavage site. These magnesium ions compensate the negative charges at both phosphate groups after phosphoryl transfer and contribute to the stabilization of the reaction intermediate.
About this Structure
1DAK is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Snapshot of a phosphorylated substrate intermediate by kinetic crystallography., Kack H, Gibson KJ, Lindqvist Y, Schneider G, Proc Natl Acad Sci U S A. 1998 May 12;95(10):5495-500. PMID:9576910
Page seeded by OCA on Thu Mar 20 10:35:25 2008
